As in the traditional production of cheese in lambskin sacks raw cow’s or sheep’s milk is mostly used, the purpose of this study is to see how the production affects the microbiological quality of the cheese. To do that, we tested 39 samples of raw cow’s and sheep’s milk, curd, ripened cheese 15, 30 and 45 days and lambskin sacks for native microbial population. Two-thirds of the milk, curd and cheese samples had higher counts of staphylococci and enterobacteria than permitted by regulations. Not a single sample had Salmonella and Listeria monocytogenes, but we did find Escherichia coli in sheep’s milk and cheese, and yeast and mould in both types of milk and cheese. Staphylococcus xylosus prevailed in lambskin sacks. Despite the high incidence of S. aureus, even in the final product, staphylococcal enterotoxin was detected in only two sheep’s cheese samples. Among the lactic acid bacteria, Lactococcus lactis and Lactobacillus paracasei prevailed in cow’s cheese, whereas Leuconostoc mesenteroides and Lactobacillus plantarum prevailed in sheep’s cheese. In the lambskin sacks Leuconostoc mesenteroides and Lactobacillus plantarum were predominant. Our findings give an important insight into the fermentation and microbial ecology of the cheese in lambskin sacks.